SMTL ID : 5g3s.1

The structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum - Samarium derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

11 x SM: SAMARIUM (III) ION(Non-covalent)

SM.1: 3 residues within 4Å: Chain A: E.329 Chain B: R.40, R.206 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.329, A:E.329, H2O.7 SM.2: 3 residues within 4Å: Chain A: H.102, K.106 Ligands: CL.19 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.102, H2O.7 SM.3: 5 residues within 4Å: Chain A: A.365, H.366 Ligands: NO3.17, CL.18, TRS.20 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.366 SM.4: 2 residues within 4Å: Chain A: H.102, Q.105 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.102 SM.5: 1 residues within 4Å: Chain A: H.121 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.121 SM.6: 3 residues within 4Å: Chain A: K.7, Q.8, R.40 No protein-ligand interaction detected (PLIP) SM.7: 2 residues within 4Å: Chain A: Y.148, H.168 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.168 SM.21: 2 residues within 4Å: Chain B: H.102, K.106 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.102, H2O.15 SM.22: 6 residues within 4Å: Chain B: S.249, A.365, H.366 Ligands: NO3.33, CL.34, TRS.35 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.366 SM.23: 3 residues within 4Å: Chain B: Y.148, H.168, Y.314 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.168 SM.24: 2 residues within 4Å: Chain B: E.120, H.121 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.121, H2O.11, H2O.15

12 x HG: MERCURY (II) ION(Non-covalent)

HG.8: 8 residues within 4Å: Chain A: S.20, G.21, C.24, I.243, A.245, C.392, A.410, A.413 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.24, A:C.392 HG.9: 3 residues within 4Å: Chain A: C.326, Q.337 Ligands: HG.10 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.326, H2O.6, H2O.8 HG.10: 6 residues within 4Å: Chain A: C.326, E.329, G.333, Y.334, Q.337 Ligands: HG.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.326 HG.11: 6 residues within 4Å: Chain A: I.12, L.28, L.29, C.34, L.37 Ligands: HG.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.28, A:C.34, A:C.34, H2O.1 HG.12: 7 residues within 4Å: Chain A: I.12, L.28, L.29, C.34, L.37, L.39 Ligands: HG.11 No protein-ligand interaction detected (PLIP) HG.13: 4 residues within 4Å: Chain A: F.370, C.371, A.395, C.400 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.395 HG.25: 8 residues within 4Å: Chain B: S.20, G.21, C.24, I.243, A.245, C.392, A.410, A.413 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.24, B:C.392 HG.26: 7 residues within 4Å: Chain B: I.12, L.28, L.29, C.34, L.37, L.39 Ligands: HG.29 No protein-ligand interaction detected (PLIP) HG.27: 6 residues within 4Å: Chain B: C.326, E.329, G.333, Y.334, Q.337 Ligands: HG.28 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.326, H2O.14 HG.28: 5 residues within 4Å: Chain A: M.6 Chain B: C.326, Q.337 Ligands: NO3.15, HG.27 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.326 HG.29: 6 residues within 4Å: Chain B: I.12, L.28, L.29, C.34, L.37 Ligands: HG.26 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.28, B:C.34, B:C.34, H2O.8 HG.30: 3 residues within 4Å: Chain B: F.370, A.395, C.400 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.395, H2O.15

2 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.14: 41 residues within 4Å: Chain A: V.15, G.16, A.17, G.18, I.19, S.20, G.21, F.42, D.43, M.44, Q.45, G.49, G.50, R.51, I.52, L.65, G.66, A.67, G.68, R.69, Y.70, Y.211, R.212, L.213, A.245, I.246, P.247, A.250, L.254, L.272, K.274, Y.314, W.364, G.367, S.393, D.394, G.401, W.402, M.403, E.404 Ligands: TRS.20 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:L.272, A:W.364 Hydrogen bonds: A:G.18, A:S.20, A:S.20, A:S.20, A:M.44, A:G.49, A:G.50, A:R.51, A:R.51, A:G.68, A:R.69, A:R.69, A:R.69, A:L.213, A:L.213, A:D.394, A:D.394, A:W.402, A:M.403 Water bridges: A:I.19, A:G.21, A:D.43, A:D.43, A:Q.45, A:R.51, A:I.52, A:G.66, A:R.69, A:Y.314, A:S.393, A:S.393, A:S.393, A:E.404 Salt bridges: A:R.51, A:R.51 FDA.31: 41 residues within 4Å: Chain B: V.15, G.16, A.17, G.18, I.19, S.20, G.21, F.42, D.43, M.44, Q.45, G.49, G.50, R.51, I.52, L.65, G.66, A.67, G.68, R.69, Y.70, Y.211, R.212, L.213, A.245, I.246, P.247, A.250, L.254, L.272, K.274, Y.314, W.364, G.367, S.393, D.394, G.401, W.402, M.403, E.404 Ligands: TRS.35 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:L.272, B:Y.314, B:W.364 Hydrogen bonds: B:G.18, B:S.20, B:S.20, B:S.20, B:M.44, B:G.49, B:G.50, B:R.51, B:G.68, B:R.69, B:R.69, B:R.69, B:L.213, B:L.213, B:D.394, B:M.403 Water bridges: B:I.19, B:I.19, B:G.21, B:D.43, B:D.43, B:Q.45, B:R.51, B:R.51, B:R.51, B:G.66, B:R.69, B:Y.314, B:S.393, B:S.393, B:E.404 Salt bridges: B:R.51, B:R.51

5 x NO3: NITRATE ION(Non-functional Binders)

NO3.15: 4 residues within 4Å: Chain A: M.6 Chain B: Y.322, Q.337 Ligands: HG.28 No protein-ligand interaction detected (PLIP) NO3.16: 8 residues within 4Å: Chain A: Q.45, R.53, K.362, Y.363, W.364 Chain B: D.231 Ligands: NO3.17, TRS.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.45, A:R.53, A:K.362 NO3.17: 8 residues within 4Å: Chain A: A.365, H.366 Chain B: D.231, G.232 Ligands: SM.3, NO3.16, CL.18, TRS.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.365 NO3.32: 7 residues within 4Å: Chain A: D.231 Chain B: Q.45, R.53, K.362, W.364 Ligands: NO3.33, TRS.35 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.45, B:R.53, B:K.362 Water bridges: B:R.53 NO3.33: 8 residues within 4Å: Chain A: D.231, G.232 Chain B: A.365, H.366 Ligands: SM.22, NO3.32, CL.34, TRS.35 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.231, B:A.365

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 8 residues within 4Å: Chain A: R.51, W.364, A.365, H.366, G.367 Ligands: SM.3, NO3.17, TRS.20 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: H.102, K.106, Q.134 Ligands: SM.2 Ligand excluded by PLIP CL.34: 8 residues within 4Å: Chain B: R.51, W.364, A.365, H.366, G.367 Ligands: SM.22, NO3.33, TRS.35 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.20: 13 residues within 4Å: Chain A: M.44, Q.45, I.246, P.247, S.249, A.250, H.366, E.369 Ligands: SM.3, FDA.14, NO3.16, NO3.17, CL.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.249 Water bridges: A:E.369 TRS.35: 13 residues within 4Å: Chain B: M.44, Q.45, I.246, P.247, S.249, A.250, H.366, E.369 Ligands: SM.22, FDA.31, NO3.32, NO3.33, CL.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.249 Water bridges: B:Q.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuller, J. et al., Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum. J.Biol.Chem. (2016)

Release Date

2016-08-03

Peptides

L-TRYPTOPHAN OXIDASE VIOA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-TRYPTOPHAN OXIDASE VIOA

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